If so, maybe Freesurfer is deleting files and/or changing file permissions there - causing Matlab to subsequently complain. I would not expect multiple programs writing to the same directory tree to work together if they use different file permissions, privileges, and/or perform independent clean/delete functions in shared directories.

- R.

On Jan 9, 2024, at 14:47, Michael Ruvalcaba <michaelruvalcaba@berkeley.edu> wrote:

External Email - Use Caution

Hello,

I am trying to run the recon -all function in my MATLAB pipeline using Freesurfer 6.0.0 and I have no issues with it. However, when I run the recon -all step using Freesurfer 7.2.0 and run the following command (the recon -all step finishes without error by the way):

ft_read_mri([subdir '3D_Images/freesurfer_pre-op/freesurfer/mri/T1.mgz']);

I get the following error:

/bin/bash: /scratch/tp746feb5d_1e83_4141_b25d_1824a1cb209e.load_mgh.m.mgh: Permission denied

The issue is there is no scratch file and it looks like between version 6.0.0 and 7.2.0 there is some extra lines of code that uses a scratch directory (which 6.0.0 doesn't)

Does anyone have any input on this? I hope this made sense!

Best,
Michael Ruvalcaba
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard..edu/mailman/listinfo/freesurfer